Hi J,
I can't reproduce the problem. I do the following:
Load your .tgd file: The two fractals you highlighted have smallest scale = 50, octaves = 7. I take it that these are the values you want.
Load your .tgd file, set the smallest scale to 79, which results in octaves = 6. Save a new .tgd file. Load the new file, and the values are exactly how I saved them (79 and 6).
Load your .tgd file (which has 50 and 7). Copy the sphere, paste. Inside the copy, the values still are 50 and 7. Save a clip file from this, reinsert the clip file. The values in the inserted clip file are 50 and 7.
Is there something else I should try? Maybe there's still a bug somewhere which caused things to change, but I can't figure out where in your steps that happened. The only thing that I know will change the smallest scale to 79.8459 is manually changing the number of octaves to 6, but I don't know how that happened.
[Update: the number 79.84589974 is in your clip file, so if there is a bug it must have happened before saving the clip file or during the save]
Matt